Runnable code:
library(cola)
library(scRNAseq)
data = ReprocessedFluidigmData()
anno = colData(data)[, c("Biological_Condition", "Coverage_Type", "Cluster1", "Cluster2")]
anno = as.data.frame(anno)
mat = assays(data)$rsem_tpm[, anno$Coverage_Type == "High"]
count = assays(data)$rsem_counts[, anno$Coverage_Type == "High"]
l = apply(count, 1, function(x) sum(x > 0)/length(x) > 0.1)
mat = log2(mat[l, ] + 1)
mat = adjust_matrix(mat)
anno = anno[anno$Coverage_Type == "High", ]
rh = hierarchical_partition(mat, cores = 4, anno = anno)
saveRDS(rh, file = "Fluidigm_cola_rh.rds")
cola_report(rh, output = "Fluidigm_cola_rh_report", title = "cola Report for Hierarchical Partitioning - 'Fluidigm'")
The HTML report is here. (generated by cola version 2.0.0, R 4.1.0.)